[2023-03-18 04:16:54,163] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:54,163] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:54,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg5885dbfe-31b4-45ac-b045-9cebbe903104/dqc_reference
[2023-03-18 04:16:55,839] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:55,839] [INFO] Task started: Prodigal
[2023-03-18 04:16:55,839] [INFO] Running command: cat /var/lib/cwl/stg50ebad90-d22e-4bfa-a195-9f5295f89b23/OceanDNA-b440.fa | prodigal -d OceanDNA-b440/cds.fna -a OceanDNA-b440/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:13,444] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:13,444] [INFO] Task started: HMMsearch
[2023-03-18 04:17:13,444] [INFO] Running command: hmmsearch --tblout OceanDNA-b440/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5885dbfe-31b4-45ac-b045-9cebbe903104/dqc_reference/reference_markers.hmm OceanDNA-b440/protein.faa > /dev/null
[2023-03-18 04:17:13,651] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:13,652] [INFO] Found 6/6 markers.
[2023-03-18 04:17:13,671] [INFO] Query marker FASTA was written to OceanDNA-b440/markers.fasta
[2023-03-18 04:17:13,672] [INFO] Task started: Blastn
[2023-03-18 04:17:13,673] [INFO] Running command: blastn -query OceanDNA-b440/markers.fasta -db /var/lib/cwl/stg5885dbfe-31b4-45ac-b045-9cebbe903104/dqc_reference/reference_markers.fasta -out OceanDNA-b440/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:14,304] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:14,305] [INFO] Selected 20 target genomes.
[2023-03-18 04:17:14,305] [INFO] Target genome list was writen to OceanDNA-b440/target_genomes.txt
[2023-03-18 04:17:14,341] [INFO] Task started: fastANI
[2023-03-18 04:17:14,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ebad90-d22e-4bfa-a195-9f5295f89b23/OceanDNA-b440.fa --refList OceanDNA-b440/target_genomes.txt --output OceanDNA-b440/fastani_result.tsv --threads 1
[2023-03-18 04:17:27,662] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:27,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5885dbfe-31b4-45ac-b045-9cebbe903104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:27,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5885dbfe-31b4-45ac-b045-9cebbe903104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:27,668] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:27,668] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:17:27,668] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.8075	345	901	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.0522	251	901	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.7508	192	901	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.6003	143	901	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.7173	72	901	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.5118	79	901	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:27,669] [INFO] DFAST Taxonomy check result was written to OceanDNA-b440/tc_result.tsv
[2023-03-18 04:17:27,669] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:27,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:27,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5885dbfe-31b4-45ac-b045-9cebbe903104/dqc_reference/checkm_data
[2023-03-18 04:17:27,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:27,674] [INFO] Task started: CheckM
[2023-03-18 04:17:27,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b440/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b440/checkm_input OceanDNA-b440/checkm_result
[2023-03-18 04:18:14,454] [INFO] Task succeeded: CheckM
[2023-03-18 04:18:14,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:18:14,541] [INFO] ===== Completeness check finished =====
[2023-03-18 04:18:14,541] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:18:14,541] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b440/markers.fasta)
[2023-03-18 04:18:14,542] [INFO] Task started: Blastn
[2023-03-18 04:18:14,542] [INFO] Running command: blastn -query OceanDNA-b440/markers.fasta -db /var/lib/cwl/stg5885dbfe-31b4-45ac-b045-9cebbe903104/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b440/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:18:15,630] [INFO] Task succeeded: Blastn
[2023-03-18 04:18:15,631] [INFO] Selected 18 target genomes.
[2023-03-18 04:18:15,631] [INFO] Target genome list was writen to OceanDNA-b440/target_genomes_gtdb.txt
[2023-03-18 04:18:15,740] [INFO] Task started: fastANI
[2023-03-18 04:18:15,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ebad90-d22e-4bfa-a195-9f5295f89b23/OceanDNA-b440.fa --refList OceanDNA-b440/target_genomes_gtdb.txt --output OceanDNA-b440/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:18:25,253] [INFO] Task succeeded: fastANI
[2023-03-18 04:18:25,261] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:18:25,261] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_905182555.1	s__Ilumatobacter_A sp905182555	99.0734	677	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018666235.1	s__Ilumatobacter_A sp018666235	78.3941	398	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	77.816	344	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.8058	278	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711735.1	s__Ilumatobacter_A sp002711735	77.1987	153	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.50	99.50	0.82	0.82	2	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	77.0417	252	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	76.7508	192	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	76.6304	153	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015767405.1	s__Sva-07 sp015767405	76.5038	113	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Sva-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969685.1	s__UBA3006 sp018969685	76.3965	69	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090765.1	s__Sva-07 sp019090765	76.2021	65	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Sva-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	75.7059	75	901	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:18:25,262] [INFO] GTDB search result was written to OceanDNA-b440/result_gtdb.tsv
[2023-03-18 04:18:25,264] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:18:25,268] [INFO] DFAST_QC result json was written to OceanDNA-b440/dqc_result.json
[2023-03-18 04:18:25,268] [INFO] DFAST_QC completed!
[2023-03-18 04:18:25,268] [INFO] Total running time: 0h1m31s